See also: Cloudflare in front of Mastodon.

A lot of naive Mastodon admins are putting default Cloudflare configurations in front of their instances. The problem is that inter-instance requests necessary for federation then get caught as bots (because they essentially are) and connections in the network degrade, causing eventual de-federation.

Cloudflare is magic, in the good and bad ways. I'd only use it for very small personal sites or things that can afford downtime and don't need integrations, or for large businesses that can afford the enterprise plans and will actively manage the account and respond to business and tech needs with config changes.